Please help ......
Have installed Myrna 1.2.1 on Hadoop cluster (0.20) with Bowtie 1.0.0, R/BioConductor and SRA toolkits. All required env variables have been set. Install tests pass fine. When running the Yeast (small) job, ends in an error in the Step 2 (Align). I have tired the same test with Bowtie 0.12.8, with the same result.
I have seen similar errors when I was not using the right version of Bowtie before for Crossbow (0.12.8), but release notes for Myrna 1.2.1 mentions BT 1.0.0.
Excerpt from the logs:
lrwxrwxrwx 1 mapred mapred 84 Aug 20 11:08 job.jar -> /hdfs/hd1/hadoop/mapred/taskTracker/root/jobcache/job_201307291643_0023/jars/job.jar
drwxr-xr-x 2 mapred mapred 4096 Aug 20 11:08 tmp
Align.pl: Read first line of stdin:
FN:SRR014339.fastq;LB:rrp6_lsm1_pat1-1;RN:@SRR014339.4500001 CGCAAGTCATCAGCTTGCGTTGATTACGTCCCAGAT `````_`T```Z`[P`OQ`PQZPMNPKDDDKC@A>F
java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 143
at org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:362)
at org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:575)
at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:135)
at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:57)
at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:36)
at org.apache.hadoop.mapred.MapTask.runOldMapper_aroundBody2(MapTask.java:444)
at org.apache.hadoop.mapred.MapTask$AjcClosure3.run(MapTask.java:1)
at org.aspectj.runtime.reflect.JoinPointImpl.proceed(JoinPointImpl.java:149)
at com.intel.bigdata.management.agent.HadoopTaskAspect.doPhaseCall(HadoopTaskAspect.java:166)
at com.intel.bigdata.management.agent.HadoopTaskAspect.ajc$inlineAccessMethod$com_intel_bigdata_management_agent_HadoopTaskAspect$com_intel_bigdata_management_agent_HadoopTaskAspect$doPhaseCall(HadoopTaskAspect.java:1)
at com.intel.bigdata.management.agent.HadoopTaskAspect.aroundMap(HadoopTaskAspect.java:38)
at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:417)
at org.apache.hadoop.mapred.MapTask.run_aroundBody0(MapTask.java:377)
at org.apache.hadoop.mapred.MapTask$AjcClosure1.run(MapTask.java:1)
at org.aspectj.runtime.reflect.JoinPointImpl.proceed(JoinPointImpl.java:149)
at com.intel.bigdata.management.agent.HadoopTaskAspect.aroundTaskRun(HadoopTaskAspect.java:95)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:351)
at org.apache.hadoop.mapred.Child$4.run(Child.java:266)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1132)
at org.apache.hadoop.mapred.Child.main(Child.java:260)
Have installed Myrna 1.2.1 on Hadoop cluster (0.20) with Bowtie 1.0.0, R/BioConductor and SRA toolkits. All required env variables have been set. Install tests pass fine. When running the Yeast (small) job, ends in an error in the Step 2 (Align). I have tired the same test with Bowtie 0.12.8, with the same result.
I have seen similar errors when I was not using the right version of Bowtie before for Crossbow (0.12.8), but release notes for Myrna 1.2.1 mentions BT 1.0.0.
Excerpt from the logs:
lrwxrwxrwx 1 mapred mapred 84 Aug 20 11:08 job.jar -> /hdfs/hd1/hadoop/mapred/taskTracker/root/jobcache/job_201307291643_0023/jars/job.jar
drwxr-xr-x 2 mapred mapred 4096 Aug 20 11:08 tmp
Align.pl: Read first line of stdin:
FN:SRR014339.fastq;LB:rrp6_lsm1_pat1-1;RN:@SRR014339.4500001 CGCAAGTCATCAGCTTGCGTTGATTACGTCCCAGAT `````_`T```Z`[P`OQ`PQZPMNPKDDDKC@A>F
java.lang.RuntimeException: PipeMapRed.waitOutputThreads(): subprocess failed with code 143
at org.apache.hadoop.streaming.PipeMapRed.waitOutputThreads(PipeMapRed.java:362)
at org.apache.hadoop.streaming.PipeMapRed.mapRedFinished(PipeMapRed.java:575)
at org.apache.hadoop.streaming.PipeMapper.close(PipeMapper.java:135)
at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:57)
at org.apache.hadoop.streaming.PipeMapRunner.run(PipeMapRunner.java:36)
at org.apache.hadoop.mapred.MapTask.runOldMapper_aroundBody2(MapTask.java:444)
at org.apache.hadoop.mapred.MapTask$AjcClosure3.run(MapTask.java:1)
at org.aspectj.runtime.reflect.JoinPointImpl.proceed(JoinPointImpl.java:149)
at com.intel.bigdata.management.agent.HadoopTaskAspect.doPhaseCall(HadoopTaskAspect.java:166)
at com.intel.bigdata.management.agent.HadoopTaskAspect.ajc$inlineAccessMethod$com_intel_bigdata_management_agent_HadoopTaskAspect$com_intel_bigdata_management_agent_HadoopTaskAspect$doPhaseCall(HadoopTaskAspect.java:1)
at com.intel.bigdata.management.agent.HadoopTaskAspect.aroundMap(HadoopTaskAspect.java:38)
at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:417)
at org.apache.hadoop.mapred.MapTask.run_aroundBody0(MapTask.java:377)
at org.apache.hadoop.mapred.MapTask$AjcClosure1.run(MapTask.java:1)
at org.aspectj.runtime.reflect.JoinPointImpl.proceed(JoinPointImpl.java:149)
at com.intel.bigdata.management.agent.HadoopTaskAspect.aroundTaskRun(HadoopTaskAspect.java:95)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:351)
at org.apache.hadoop.mapred.Child$4.run(Child.java:266)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:396)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1132)
at org.apache.hadoop.mapred.Child.main(Child.java:260)
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